StackReg Error- Please help!

fiji
imagej
macro
stack

#1

I was wondering if anyone could help try to figure out an error I keep on getting when trying to run the StackReg plugin to an nd2 time stack file in Fiji. I have downloaded TurboReg as indicated on the BIG website.

Below is the console message that I get including the error (bolded).

Any help would be appreciated!

Searching for blocks
Parsing block 'ND2 FILE SIG' 0%
Parsing block 'ImageMetadat' 0%
Parsing block 'ImageCalibra' 0%
Parsing block 'ImageMetadat' 0%
Parsing block 'ImageCalibra' 0%
Parsing block 'ImageMetadat' 0%
Parsing block 'ImageAttribu' 0%
Parsing block 'ImageDataSeq' 0%
Parsing block 'ImageDataSeq' 0%
Parsing block 'ImageDataSeq' 2%
Parsing block 'ImageDataSeq' 4%
Parsing block 'ImageDataSeq' 6%
Parsing block 'ImageDataSeq' 8%
Parsing block 'ImageDataSeq' 10%
Parsing block 'ImageDataSeq' 13%
Parsing block 'ImageDataSeq' 15%
Parsing block 'ImageDataSeq' 17%
Parsing block 'ImageDataSeq' 19%
Parsing block 'ImageDataSeq' 21%
Parsing block 'ImageDataSeq' 23%
Parsing block 'ImageDataSeq' 26%
Parsing block 'ImageDataSeq' 28%
Parsing block 'ImageDataSeq' 30%
Parsing block 'ImageDataSeq' 32%
Parsing block 'ImageDataSeq' 34%
Parsing block 'ImageDataSeq' 36%
Parsing block 'ImageDataSeq' 39%
Parsing block 'ImageDataSeq' 41%
Parsing block 'ImageDataSeq' 43%
Parsing block 'ImageDataSeq' 45%
Parsing block 'ImageDataSeq' 47%
Parsing block 'ImageDataSeq' 49%
Parsing block 'ImageDataSeq' 52%
Parsing block 'ImageDataSeq' 54%
Parsing block 'ImageDataSeq' 56%
Parsing block 'ImageDataSeq' 58%
Parsing block 'ImageDataSeq' 60%
Parsing block 'ImageDataSeq' 63%
Parsing block 'ImageDataSeq' 65%
Parsing block 'ImageDataSeq' 67%
Parsing block 'ImageDataSeq' 69%
Parsing block 'ImageDataSeq' 71%
Parsing block 'ImageDataSeq' 73%
Parsing block 'ImageDataSeq' 76%
Parsing block 'ImageDataSeq' 78%
Parsing block 'ImageDataSeq' 80%
Parsing block 'ImageDataSeq' 82%
Parsing block 'ImageDataSeq' 84%
Parsing block 'ImageDataSeq' 86%
Parsing block 'ImageDataSeq' 89%
Parsing block 'ImageDataSeq' 91%
Parsing block 'ImageDataSeq' 93%
Parsing block 'ImageDataSeq' 95%
Parsing block 'ImageDataSeq' 97%
Parsing block 'ImageMetadat' 99%
Parsing block 'CustomData|R' 99%
Parsing block 'ImageEventsL' 99%
Parsing block 'ImageTextInf' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'CustomData|C' 99%
Parsing block 'CustomData|C' 99%
Parsing block 'CustomData|T' 99%
Parsing block 'CustomData|A' 99%
Parsing block 'CustomData|A' 99%
Parsing block 'CustomData|A' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'ImageAttribu' 99%
Parsing block 'CustomDataVa' 99%
Parsing block 'ImageAttribu' 99%
Parsing block 'ND2 FILEMAP ' 99%
StackReg_ not up-to-date because 1 source files are not up-to-date (/var/folders/xn/pcrmv96s7fbb82c6k8ctfj080000gn/T/java909784749742982566/src/main/java/StackReg_.java)
Compiling 1 file in /var/folders/xn/pcrmv96s7fbb82c6k8ctfj080000gn/T/java909784749742982566
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xerbla-0.8.jar:/Applications/Fiji.app/jars/xercesImpl-2.8.1.jar:/Applications/Fiji.app/jars/xml-apis-ext-1.3.04.jar:/Applications/Fiji.app/jars/xmlgraphics-commons-2.3.jar:/Applications/Fiji.app/jars/xmpcore-5.1.2.jar:/Applications/Fiji.app/jars/xz-1.0.jar:/Applications/Fiji.app/jars/yecht-1.0.jar:/Applications/Fiji.app/plugins/z_spacing-1.0.3.jar:/Applications/Fiji.app/java/macosx/jdk1.8.0_172.jre/jre/Contents/Home/lib/ext/zipfs.jar, -d, /var/folders/xn/pcrmv96s7fbb82c6k8ctfj080000gn/T/java909784749742982566/target/classes, /var/folders/xn/pcrmv96s7fbb82c6k8ctfj080000gn/T/java909784749742982566/src/main/java/StackReg_.java]
using the class path: /var/folders/xn/pcrmv96s7fbb82c6k8ctfj080000gn/T/java909784749742982566/target/classes:/Applications/Fiji.app/plugins/3D_Blob_Segmentation-3.0.1.jar:/Applications/Fiji.app/plugins/3D_Objects_Counter-2.0.1.jar:/Applications/Fiji.app/plugins/3D_Viewer-4.0.2.jar:/Applications/Fiji.app/plugins/AnalyzeSkeleton_-3.2.2.jar:/Applications/Fiji.app/plugins/Anisotropic_Diffusion_2D-2.0.1.jar:/Applications/Fiji.app/plugins/Archipelago_Plugins-0.5.4.jar:/Applications/Fiji.app/plugins/Arrow_-2.0.2.jar:/Applications/Fiji.app/plugins/Auto_Local_Threshold-1.10.0.jar:/Applications/Fiji.app/plugins/Auto_Threshold-1.17.1.jar:/Applications/Fiji.app/plugins/BalloonSegmentation_-3.0.1.jar:/Applications/Fiji.app/plugins/Bug_Submitter-2.1.1.jar:/Applications/Fiji.app/plugins/CPU_Meter-2.0.1.jar:/Applications/Fiji.app/plugins/Calculator_Plus-2.0.1.jar:/Applications/Fiji.app/plugins/Cell_Counter-2.2.2.jar:/Applications/Fiji.app/plugins/Colocalisation_Analysis-3.0.3.jar:/Applications/Fiji.app/plugins/Color_Histogram-2.0.7.jar:/Applications/Fiji.app/plugins/Color_Inspector_3D-2.3.2.jar:/Applications/Fiji.app/plugins/Colour_Deconvolution-3.0.2.jar:/Applications/Fiji.app/plugins/CorrectBleach_-2.0.2.jar:/Applications/Fiji.app/plugins/Correct_3D_Drift-1.0.3.jar:/Applications/Fiji.app/plugins/Descriptor_based_registration-2.1.2.jar:/Applications/Fiji.app/plugins/Dichromacy_-2.1.1.jar:/Applications/Fiji.app/plugins/Directionality_-2.2.0.jar:/Applications/Fiji.app/plugins/FS_Align_TrakEM2-2.0.2.jar:/Applications/Fiji.app/plugins/Feature_Detection-2.0.2.jar:/Applications/Fiji.app/plugins/Fiji_Archipelago-2.0.1.jar:/Applications/Fiji.app/plugins/Fiji_Developer-2.0.6.jar:/Applications/Fiji.app/plugins/Fiji_Package_Maker-2.1.1.jar:/Applications/Fiji.app/plugins/Fiji_Plugins-3.1.1.jar:/Applications/Fiji.app/plugins/FlowJ_-1.29.3.jar:/Applications/Fiji.app/plugins/Graph_Cut-1.0.2.jar:/Applications/Fiji.app/plugins/Gray_Morphology-2.3.4.jar:/Applications/Fiji.app/plugins/H5J_Loader_Plugin-1.0.7.jar:/Applications/Fiji.app/plugins/Helmholtz_Analysis-2.0.2.jar:/Applications/Fiji.app/plugins/IJ_Robot-2.0.1.jar:/Applications/Fiji.app/plugins/IO_-3.0.4.jar:/Applications/Fiji.app/plugins/Image_5D-2.0.2.jar:/Applications/Fiji.app/plugins/Image_Expression_Parser-3.0.1.jar:/Applications/Fiji.app/plugins/Interactive_3D_Surface_Plot-3.0.0.jar:/Applications/Fiji.app/plugins/IsoData_Classifier-2.0.1.jar:/Applications/Fiji.app/jars/JWlz-1.4.0.jar:/Applications/Fiji.app/plugins/Kuwahara_Filter-2.0.1.jar:/Applications/Fiji.app/plugins/KymographBuilder-2.0.0.jar:/Applications/Fiji.app/plugins/LSM_Reader-4.1.2.jar:/Applications/Fiji.app/plugins/LSM_Toolbox-4.1.2.jar:/Applications/Fiji.app/plugins/Lasso_and_Blow_Tool-2.0.2.jar:/Applications/Fiji.app/plugins/Linear_Kuwahara-2.0.1.jar:/Applications/Fiji.app/plugins/LocalThickness_-4.0.2.jar:/System/Library/Java/Extensions/MRJToolkit.jar:/Applications/Fiji.app/plugins/MTrack2_-2.0.1.jar:/Applications/Fiji.app/plugins/M_I_P-2.0.1.jar:/Applications/Fiji.app/plugins/Manual_Tracking-2.1.1.jar:/Applications/Fiji.app/plugins/Multi_Kymograph-...

#2

How are you running StackReg?

StackReg is available in Fiji via the BIG-EPFL update site (it is shipped in the file plugins/StackReg_-2.0.0.jar).

Please don’t install any .java file manually, and don’t try running StackReg as Java code from the script editor, as this requires the Java code to be compiled, which is not supported by the standard Fiji, as it comes bundled with a Java runtime enviroment (JRE), not a JDK.


#3

The link your provided seemed to give me a different .java file than what was on the BIG website, which seems to work! Thanks for the info.


#4

Indeed. The version on the BIG website seems to be from 2011, whereas the update site shipping with Fiji – as well as the accompanying source repository – contain some newer additions to make the plugin compatible with Fiji’s distribution mechanism.